QUAGMIRE v1.3: a quasi-geostrophic model for investigating rotating fluids experiments

QUAGMIRE is a quasi-geostrophic numerical model for performing fast, high-resolution simulations of multi-layer rotating annulus laboratory experiments on a desktop personal computer. The model uses a hybrid finite-difference/spectral approach to numerically integrate the coupled nonlinear partial differential equations of motion in cylindrical geometry in each layer. Version 1.3 implements the special case of two fluid layers of equal resting depths. The flow is forced either by a differentially rotating lid, or by relaxation to specified streamfunction or potential vorticity fields, or both. Dissipation is achieved through Ekman layer pumping and suction at the horizontal boundaries, including the internal interface. The effects of weak interfacial tension are included, as well as the linear topographic beta-effect and the quadratic centripetal beta-effect. Stochastic forcing may optionally be activated, to represent approximately the effects of random unresolved features. A leapfrog time stepping scheme is used, with a Robert filter. Flows simulated by the model agree well with those observed in the corresponding laboratory experiments.

Simultaneous analysis of v1, v4, 2v2, v2+v5, and 2v5 bands of 12CH3F

The Fourier-transform spectrum of CH3F from 2800 to 3100 cm−1, obtained by Guelachvili in Orsay at a resolution of about 0.003 cm−1, was analyzed. The effective Hamiltonian used contained all symmetry allowed interactions up to second order in the Amat-Nielsen classification, together with selected third-order terms, amongst the set of nine vibrational basis functions represented by the states ν1(A1), ν4(E), 2ν2(A1), ν2 + ν5(E), 2ν50(A1), and 2ν5±2(E). A number of strong Fermi and Coriolis resonances are involved. The vibrational Hamiltonian matrix was not factorized beyond the requirements of symmetry. A total of 59 molecular parameters were refined in a simultaneous least-squares analysis to over 1500 upper-state energy levels for J ≤ 20 with a standard deviation of 0.013 cm−1. Although the standard deviation remains an order of magnitude greater than the precision of the measurements, this work breaks new ground in the simultaneous analysis of interacting symmetric top vibrational levels, in terms of the number of interacting vibrational states and the number of parameters in the Hamiltonian.

Molecular t-matrices for low-energy electron diffraction (TMOL v1.1)*1

We describe a FORTRAN-90 program that computes scattering t-matrices for a molecule. These can be used in a Low-Energy Electron Diffraction program to solve the molecular structural problem very efficiently. The intramolecular multiple scattering is computed within a Dyson-like approach, using free space Green propagators in a basis of spherical waves. The advantage of this approach is related to exploiting the chemical identity of the molecule, and to the simplicity to translate and rotate these t-matrices without performing a new multiple-scattering calculation for each configuration. FORTRAN-90 routines for rotating the resulting t-matrices using Wigner matrices are also provided.

A FORTRAN-90 low-energy electron diffraction program (LEED90 v1.1)

We describe a FORTRAN-90 program to compute low-energy electron diffraction I(V) curves. Plane-waves and layer doubling are used to compute the inter-layer multiple-scattering, while the intra-layer multiple-scattering is computed in the standard way expanding the wavefield on a basis of spherical waves. The program is kept as general as possible, in order to allow testing different parts of multiple-scattering calculations. In particular, it can handle non-diagonal t-matrices describing the scattering of non-spherical potentials, anisotropic vibrations, anharmonicity, etc. The program does not use old FORTRAN flavours, and has been written keeping in mind the advantage for parallelism brought forward by FORTRAN-90.

Aircraft routing with minimal climate impact: the REACT4C climate cost function modelling approach (V1.0)

In addition to CO2, the climate impact of aviation is strongly influenced by non-CO2 emissions, such as nitrogen oxides, influencing ozone and methane, and water vapour, which can lead to the formation of persistent contrails in ice-supersaturated regions. Because these non-CO2 emission effects are characterised by a short lifetime, their climate impact largely depends on emission location and time; that is to say, emissions in certain locations (or times) can lead to a greater climate impact (even on the global average) than the same emission in other locations (or times). Avoiding these climate-sensitive regions might thus be beneficial to climate. Here, we describe a modelling chain for investigating this climate impact mitigation option. This modelling chain forms a multi-step modelling approach, starting with the simulation of the fate of emissions released at a certain location and time (time-region grid points). This is performed with the chemistry–climate model EMAC, extended via the two submodels AIRTRAC (V1.0) and CONTRAIL (V1.0), which describe the contribution of emissions to the composition of the atmosphere and to contrail formation, respectively. The impact of emissions from the large number of time-region grid points is efficiently calculated by applying a Lagrangian scheme. EMAC also includes the calculation of radiative impacts, which are, in a second step, the input to climate metric formulas describing the global climate impact of the emission at each time-region grid point. The result of the modelling chain comprises a four-dimensional data set in space and time, which we call climate cost functions and which describes the global climate impact of an emission at each grid point and each point in time. In a third step, these climate cost functions are used in an air traffic simulator (SAAM) coupled to an emission tool (AEM) to optimise aircraft trajectories for the North Atlantic region. Here, we describe the details of this new modelling approach and show some example results. A number of sensitivity analyses are performed to motivate the settings of individual parameters. A stepwise sanity check of the results of the modelling chain is undertaken to demonstrate the plausibility of the climate cost functions.

Including an ocean carbon cycle model into iLOVECLIM (v1.0)

The atmospheric carbon dioxide concentration plays a crucial role in the radiative balance and as such has a strong influence on the evolution of climate. Because of the numerous interactions between climate and the carbon cycle, it is necessary to include a model of the carbon cycle within a climate model to understand and simulate past and future changes of the carbon cycle. In particular, natural variations of atmospheric CO2 have happened in the past, while anthropogenic carbon emissions are likely to continue in the future. To study changes of the carbon cycle and climate on timescales of a few hundred to a few thousand years, we have included a simple carbon cycle model into the iLOVECLIM Earth System Model. In this study, we describe the ocean and terrestrial biosphere carbon cycle models and their performance relative to observational data. We focus on the main carbon cycle variables including the carbon isotope ratios δ13C and the Δ14C. We show that the model results are in good agreement with modern observations both at the surface and in the deep ocean for the main variables, in particular phosphates, dissolved inorganic carbon and the carbon isotopes.

The infrared spectrum of silicon difluoride

The infrared spectrum of the stretching fundamentals of SiF2 has been obtained at a resolution of ≈ 0.1 cm−1 using a FTIR spectrometer. The spectrum has been analysed using computer simulation based on a coupled hamiltonian for v1 and v3, giving v1 = 855.01 cm−1 and v3 = 870.40 cm−1. The relative magnitude and sign of the vibrational transition moments has been determined from the ξC13 Coriolis coupling.

Prediction of global and local model quality in CASP8 using the ModFOLD server

The development of effective methods for predicting the quality of three-dimensional (3D) models is fundamentally important for the success of tertiary structure (TS) prediction strategies. Since CASP7, the Quality Assessment (QA) category has existed to gauge the ability of various model quality assessment programs (MQAPs) at predicting the relative quality of individual 3D models. For the CASP8 experiment, automated predictions were submitted in the QA category using two methods from the ModFOLD server-ModFOLD version 1.1 and ModFOLDclust. ModFOLD version 1.1 is a single-model machine learning based method, which was used for automated predictions of global model quality (QMODE1). ModFOLDclust is a simple clustering based method, which was used for automated predictions of both global and local quality (QMODE2). In addition, manual predictions of model quality were made using ModFOLD version 2.0-an experimental method that combines the scores from ModFOLDclust and ModFOLD v1.1. Predictions from the ModFOLDclust method were the most successful of the three in terms of the global model quality, whilst the ModFOLD v1.1 method was comparable in performance to other single-model based methods. In addition, the ModFOLDclust method performed well at predicting the per-residue, or local, model quality scores. Predictions of the per-residue errors in our own 3D models, selected using the ModFOLD v2.0 method, were also the most accurate compared with those from other methods. All of the MQAPs described are publicly accessible via the ModFOLD server at: http://www.reading.ac.uk/bioinf/ModFOLD/. The methods are also freely available to download from: http://www.reading.ac.uk/bioinf/downloads/.

The automation of nested clade phylogeographic analysis

ANeCA is a fully automated implementation of Nested Clade Phylogeographic Analysis. This was originally developed by Templeton and colleagues, and has been used to infer, from the pattern of gene sequence polymorphisms in a geographically structured population, the historical demographic processes that have shaped its evolution. Until now it has been necessary to perform large parts of the procedure manually. We provide a program that will take data in Nexus sequential format, and directly output a set of inferences. The software also includes TCS v1.18 and GeoDis v2.2 as part of automation.

In vitro three-stage continuous fermentation of gluco-oligosaccharides produced by Gluconobacter oxydans NCIMB 4943 by the human colonic microflora

Gluco-oligosaccharides produced by Gluconobacter oxydans NCIMB 4943 from maltodextrin as the source, were evaluated for their fermentability by the human colonic microflora. The selectivity of growth of desirable bacteria in the human colon was studied in a three-stage continuous model of the human large intestine. Populations of bacteria, and their fluctuations as a response to the fermentation, were enumerated using fluorescent in situ hybridization (FISH). The gluco-oligosaccharides resulted in increases in numbers of bifidobacteria and the Lactobacillus/Enterococcus group in all 3 vessels of the system, representing the proximal, transverse and distal colonic areas. The prebiotic indices of the glucooligosaccharides were 2.29, 4.23 and 2.74 in V1, V2 and V3 respectively.

The temporal impulse response underlying saccadic decisions

Models of perceptual decision making often assume that sensory evidence is accumulated over time in favor of the various possible decisions, until the evidence in favor of one of them outweighs the evidence for the others. Saccadic eye movements are among the most frequent perceptual decisions that the human brain performs. We used stochastic visual stimuli to identify the temporal impulse response underlying saccadic eye movement decisions. Observers performed a contrast search task, with temporal variability in the visual signals. In experiment 1, we derived the temporal filter observers used to integrate the visual information. The integration window was restricted to the first similar to 100 ms after display onset. In experiment 2, we showed that observers cannot perform the task if there is no useful information to distinguish the target from the distractor within this time epoch. We conclude that (1) observers did not integrate sensory evidence up to a criterion level, (2) observers did not integrate visual information up to the start of the saccadic dead time, and (3) variability in saccade latency does not correspond to variability in the visual integration period. Instead, our results support a temporal filter model of saccadic decision making. The temporal impulse response identified by our methods corresponds well with estimates of integration times of V1 output neurons.

Texture segmentation in Williams syndrome

Williams syndrome (WS) is a developmental disorder in which visuo-spatial cognition is poor relative to verbal ability. At the level of visuo-spatial perception, individuals with WS can perceive both the local and global aspects of an image. However, the manner in which local elements are integrated into a global whole is atypical, with relative strengths in integration by luminance, closure, and alignment compared to shape, orientation and proximity. The present study investigated the manner in which global images are segmented into local parts. Segmentation by seven gestalt principles was investigated: proximity, shape, luminance, orientation, closure, size (and alignment: Experiment I only). Participants were presented with uniform texture squares and asked to detect the presence of a discrepant patch (Experiment 1) or to identify the form of a discrepant patch as a capital E or H (Experiment 2). In Experiment 1, the pattern and level of performance of the WS group did not differ from that of typically developing controls, and was commensurate with the general level of non-verbal ability observed in WS. These results were replicated in Experiment 2, with the exception of segmentation by proximity, where individuals with WS demonstrated superior performance relative to the remaining segmentation types. Overall, the results suggest that, despite some atypical aspects of visuo-spatial perception in WS, the ability to segment a global form into parts is broadly typical in this population. In turn, this informs predictions of brain function in WS, particularly areas V1 and V4. (c) 2006 Elsevier Ltd. All rights reserved.

Mapping of domains on HIV envelope protein mediating association with calnexin and protein-disulfide isomerase.

The cell catalysts calnexin (CNX) and protein-disulfide isomerase (PDI) cooperate in establishing the disulfide bonding of the HIV envelope (Env) glycoprotein. Following HIV binding to lymphocytes, cell-surface PDI also reduces Env to induce the fusogenic conformation. We sought to define the contact points between Env and these catalysts to illustrate their potential as therapeutic targets. In lysates of Env-expressing cells, 15% of the gp160 precursor, but not gp120, coprecipitated with CNX, whereas only 0.25% of gp160 and gp120 coprecipitated with PDI. Under in vitro conditions, which mimic the Env/PDI interaction during virus/cell contact, PDI readily associated with Env. The domains of Env interacting in cellulo with CNX or in vitro with PDI were then determined using anti-Env antibodies whose binding site was occluded by CNX or PDI. Antibodies against domains V1/V2, C2, and the C terminus of V3 did not bind CNX-associated Env, whereas those against C1, V1/V2, and the CD4-binding domain did not react with PDI-associated Env. In addition, a mixture of the latter antibodies interfered with PDI-mediated Env reduction. Thus, Env interacts with intracellular CNX and extracellular PDI via discrete, largely nonoverlapping, regions. The sites of interaction explain the mode of action of compounds that target these two catalysts and may enable the design of further new competitive agents.

The effect of regional changes in anthropogenic aerosols on rainfall of the East Asian summer monsoon

The response of East Asian Summer Monsoon (EASM) precipitation to long term changes in regional anthropogenic aerosols (sulphate and black carbon) is explored in an atmospheric general circulation model, the atmospheric component of the UK High-Resolution Global Environment Model v1.2 (HiGAM). Separately, sulphur dioxide (SO2) and black carbon (BC) emissions in 1950 and 2000 over East Asia are used to drive model simulations, while emissions are kept constant at year 2000 level outside this region. The response of the EASM is examined by comparing simulations driven by aerosol emissions representative of 1950 and 2000. The aerosol radiative effects are also determined using an off-line radiative transfer model. During June, July and August, the EASM was not significantly changed as either SO2 or BC emissions increased from 1950 to 2000 levels. However, in September, precipitation is significantly decreased by 26.4% for sulphate aerosol and 14.6% for black carbon when emissions are at the 2000 level. Over 80% of the decrease is attributed to changes in convective precipitation. The cooler land surface temperature over China in September (0.8 °C for sulphate and 0.5 °C for black carbon) due to increased aerosols reduces the surface thermal contrast that supports the EASM circulation. However, mechanisms causing the surface temperature decrease in September are different between sulphate and BC experiments. In the sulphate experiment, the sulphate direct and the 1st indirect radiative effects contribute to the surface cooling. In the BC experiment, the BC direct effect is the main driver of the surface cooling, however, a decrease in low cloud cover due to the increased heating by BC absorption partially counteracts the direct effect. This results in a weaker land surface temperature response to BC changes than to sulphate changes. The resulting precipitation response is also weaker, and the responses of the monsoon circulation are different for sulphate and black carbon experiments. This study demonstrates a mechanism that links regional aerosol emission changes to the precipitation changes of the EASM, and it could be applied to help understand the future changes in EASM precipitation in CMIP5 simulations.